I've never had issues switching between track and street pads on the same rotor. I put the track pads on before going to the event. By the time I'm there I'm sure any sort of transfer layer has been wiped off. I just treated my warm up lap as such and slowly worked the brakes harder and harder bringing it up to temp. After a lap or two all felt good and no issues all weekend. This was a different car but I had Raybestos ST43/47.
I had cobb TC on my focus ST and I did not like it for autocross or similar driving. You could really feel it pulling and adding power mid corner...it was just weird. If you try it out I recommend going into the settings and setting TC at the highest settings so it's targeting a higher slip percentage. IIRC the default setting is really designed for helping put power down in a straight line and I even read that on Cobb support page. Might be best to just turn it all off.
As far as conservative tune.... ask Ed, but your pump gas tune running ~E20-E30 fuel or race gas like you said sounds like a good option to me.
Good luck/have fun